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Updated: May 14, 2026

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
Published on: September 30, 2016
An in vitro-selected RNA receptor for the GAAC loop: modular receptor for non-GNRA-type tetraloop
Junya Ishikawa1, Hiroyuki Furuta, Yoshiya Ikawa
1Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan.
Abstract:
Although artificial RNA motifs that can functionally replace the GNRA/receptor interaction, a class of RNA-RNA interacting motifs, were isolated from RNA libraries and used to generate designer RNA structures, receptors for non-GNRA tetraloops have not been found in nature or selected from RNA libraries. In this study, we report successful isolation of a receptor motif interacting with GAAC, a non-GNRA tetraloop, from randomized sequences embedded in a catalytic RNA. Biochemical characterization of the GAAC/receptor interacting motif within three structural contexts showed its binding affinity, selectivity and structural autonomy. The motif has binding affinity comparable with that of a GNRA/receptor, selectivity orthogonal to GNRA/receptors and structural autonomy even in a large RNA context. These features would be advantageous for usage of the motif as a building block for designer RNAs. The isolated motif can also be used as a query sequence to search for unidentified naturally occurring GANC receptor motifs.
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